Pre-visualization of the normalized count data before any differential analysis
Load¶
Libraries and functions¶
========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=4 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=4 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Allowing multi-threading with up to 4 threads.
preparing gene to GO mapping data... preparing IC data... preparing gene to GO mapping data... preparing IC data... preparing gene to GO mapping data... preparing IC data...
Data¶
| GF_104w_F_1_2 | GF_104w_F_2_2 | GF_104w_F_3_2 | GF_104w_M_1_2 | GF_104w_M_2_2 | GF_52w_M_1_2 | GF_52w_M_2_2 | GF_52w_M_3_2 | GF_52w_M_4_2 | GF_8w_M_1_2 | ⋯ | SPF_104w_M_14_2 | SPF_8w_F_1_2 | SPF_8w_F_3_2 | SPF_8w_F_4_2 | SPF_8w_F_5_2 | GF_8w_F_1_2 | GF_8w_F_2_2 | GF_8w_F_3_2 | GF_8w_F_4_2 | GF_8w_F_5_2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610005C13Rik | 0.0000 | 0.00000 | 0.0000 | 1.768593 | 1.259244 | 0.8418979 | 4.942785 | 5.603216 | 7.231584 | 8.47277 | ⋯ | 5.28524 | 3.500355 | 2.112002 | 2.602398 | 0.00000 | 18.24998 | 0.00000 | 2.025447 | 5.268672 | 0.00000 |
| Erg28 | 868.4015 | 749.64927 | 910.3535 | 886.064952 | 992.913601 | 508.5063502 | 530.855142 | 514.375197 | 738.344705 | 603.98749 | ⋯ | 692.36648 | 763.077332 | 744.480801 | 908.237050 | 957.79030 | 898.54336 | 682.26034 | 612.697796 | 593.252445 | 809.27852 |
| 0610009B22Rik | 1021.3276 | 1169.19730 | 1180.9991 | 1224.750457 | 1558.313990 | 1038.9020466 | 876.850113 | 1016.423320 | 877.914273 | 948.95029 | ⋯ | 1206.79653 | 1268.295198 | 1164.769254 | 1295.994415 | 1446.89758 | 1040.24912 | 1020.67017 | 1142.352254 | 959.952003 | 1094.00091 |
| 0610009L18Rik | 28.2185 | 36.20465 | 18.2253 | 20.338816 | 38.406931 | 31.9921214 | 26.691041 | 22.412863 | 4.338950 | 61.73018 | ⋯ | 45.80542 | 42.004257 | 45.408049 | 102.794738 | 72.02239 | 48.30878 | 19.58642 | 11.139960 | 45.310578 | 24.36813 |
| 0610009O20Rik | 217.5555 | 278.98879 | 266.0893 | 226.379868 | 271.996624 | 299.7156634 | 349.949200 | 395.587025 | 309.511786 | 360.69794 | ⋯ | 178.81730 | 274.194454 | 252.384272 | 227.709862 | 184.89330 | 231.88216 | 158.86764 | 271.409933 | 304.529230 | 269.33199 |
| 0610010B08Rik | 0.0000 | 0.00000 | 0.0000 | 0.000000 | 0.000000 | 0.0000000 | 0.000000 | 0.000000 | 0.000000 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.000000 | 0.000000 | 0.00000 | 0.00000 | 0.00000 | 0.000000 | 0.000000 | 0.00000 |
Sample clustering¶
Gene co-expression network analysis¶
Build network¶
- 24421
- 60
- 10219
- 60
pickSoftThreshold: will use block size 4378. pickSoftThreshold: calculating connectivity for given powers... ..working on genes 1 through 4378 of 10219 ..working on genes 4379 through 8756 of 10219 ..working on genes 8757 through 10219 of 10219 Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k. 1 2 0.144 -0.617 0.901 644.0000 6.20e+02 1390.00 2 4 0.691 -1.460 0.964 114.0000 9.21e+01 438.00 3 6 0.783 -1.840 0.970 31.1000 1.94e+01 198.00 4 8 0.790 -2.020 0.962 11.0000 5.03e+00 106.00 5 10 0.832 -1.990 0.985 4.6100 1.49e+00 63.10 6 12 0.851 -1.960 0.988 2.1900 4.90e-01 40.10 7 14 0.876 -1.890 0.988 1.1500 1.72e-01 26.70 8 16 0.886 -1.820 0.971 0.6430 6.43e-02 18.40 9 18 0.899 -1.780 0.970 0.3830 2.50e-02 13.60 10 20 0.882 -1.770 0.946 0.2400 1.02e-02 10.40 11 22 0.917 -1.720 0.984 0.1560 4.29e-03 8.11 12 24 0.902 -1.700 0.962 0.1050 1.86e-03 6.46 13 26 0.408 -2.230 0.416 0.0724 8.32e-04 5.23 14 28 0.416 -2.190 0.427 0.0514 3.76e-04 4.28 15 30 0.931 -1.630 0.984 0.0372 1.74e-04 3.55
Parameters for network construction
- Soft-thresholding power parameter: 16
- Minimum module size: 25
- Height for module merging: 0.2 (below)
- Biweight Midcorrelation
| Erg28 | 0610009B22Rik | 0610009L18Rik | 0610009O20Rik | 0610010F05Rik | 0610010K14Rik | Mettl26 | 0610012G03Rik | 0610030E20Rik | 0610037L13Rik | ⋯ | Zw10 | Zwint | Zxda | Zxdb | Zxdc | Zyg11b | Zyx | Zzef1 | Zzz3 | Hikeshi | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GF_104w_F_1_2 | 868.4015 | 1021.328 | 28.21850 | 217.5555 | 411.4439 | 1351.757 | 283.0953 | 693.6289 | 899.3508 | 449.6754 | ⋯ | 618.0761 | 1471.913 | 297.6596 | 130.1692 | 923.9282 | 1333.552 | 2864.633 | 396.8795 | 752.7967 | 668.1412 |
| GF_104w_F_2_2 | 749.6493 | 1169.197 | 36.20465 | 278.9888 | 461.0769 | 1516.336 | 207.6443 | 686.8236 | 759.2329 | 526.0323 | ⋯ | 797.5672 | 1539.763 | 243.8490 | 198.0607 | 981.7850 | 1340.637 | 3358.514 | 364.1762 | 597.3768 | 703.8610 |
| GF_104w_F_3_2 | 910.3535 | 1180.999 | 18.22530 | 266.0893 | 288.8709 | 1852.601 | 222.3486 | 868.4353 | 540.3800 | 444.6972 | ⋯ | 731.7456 | 1375.099 | 153.0925 | 171.3178 | 922.1999 | 1181.910 | 3058.205 | 209.5909 | 644.2642 | 770.9300 |
| GF_104w_M_1_2 | 886.0650 | 1224.750 | 20.33882 | 226.3799 | 278.5534 | 1551.056 | 190.1237 | 823.2799 | 525.2720 | 607.5116 | ⋯ | 466.9085 | 1752.675 | 172.4378 | 344.8756 | 683.5611 | 1295.494 | 2789.955 | 261.7517 | 944.4285 | 687.9826 |
| GF_104w_M_2_2 | 992.9136 | 1558.314 | 38.40693 | 271.9966 | 304.1073 | 1911.532 | 243.0340 | 778.8422 | 707.6949 | 586.8075 | ⋯ | 878.3224 | 1957.494 | 147.9611 | 249.3302 | 1003.6172 | 1205.726 | 2819.446 | 200.8494 | 785.1384 | 583.6594 |
| GF_52w_M_1_2 | 508.5064 | 1038.902 | 31.99212 | 299.7157 | 392.3244 | 1173.606 | 182.6919 | 589.3286 | 1047.3210 | 621.3207 | ⋯ | 768.6528 | 1397.551 | 287.9291 | 275.3006 | 924.4039 | 1674.535 | 2206.614 | 749.2892 | 1163.5029 | 493.3522 |
Calculating module eigengenes block-wise from all genes
Flagging genes and samples with too many missing values...
..step 1
....pre-clustering genes to determine blocks..
Projective K-means:
..k-means clustering..
..merging smaller clusters...
Block sizes:
gBlocks
1 2 3
4997 4015 1207
..Working on block 1 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 1 into file norm_genes_TOM-block.1.RData
....clustering..
....detecting modules..
....calculating module eigengenes..
....checking kME in modules..
..Working on block 2 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 2 into file norm_genes_TOM-block.2.RData
....clustering..
....detecting modules..
....calculating module eigengenes..
....checking kME in modules..
..Working on block 3 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 3 into file norm_genes_TOM-block.3.RData
....clustering..
....detecting modules..
No modules detected in block 3
..reassigning 1 genes from module 1 to modules with higher KME.
..reassigning 1 genes from module 9 to modules with higher KME.
..reassigning 3 genes from module 10 to modules with higher KME.
..reassigning 3 genes from module 11 to modules with higher KME.
..reassigning 1 genes from module 14 to modules with higher KME.
..merging modules that are too close..
mergeCloseModules: Merging modules whose distance is less than 0.2
Calculating new MEs...
0 1 2 3 4 5 6 7 8 9 10 11 8786 446 260 191 95 93 86 62 56 53 49 42
11
- 11 modules with between 42 and 446 genes
- 8786 genes not assigned to a module
1433
1433
Network visualization¶
TOM calculation: adjacency.. ..will use 4 parallel threads. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done.
| 0610030E20Rik | 1600020E01Rik | Zfp974 | 1700094D03Rik | Lrmda | 1810026B05Rik | Ndufaf8 | 2010107E04Rik | 2210016L21Rik | 2310033P09Rik | ⋯ | Zmpste24 | Zmym6 | Znhit2 | Znrd1 | Znrf1 | Znrf2 | Zrsr2 | Zscan26 | Zswim8 | Zzef1 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610030E20Rik | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| 1600020E01Rik | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 |
| Zfp974 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1700094D03Rik | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| Lrmda | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1810026B05Rik | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 |
Module analysis¶
446
[1] 1
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
11757 GO:0044446 3.822525e-17 1 234
3148 GO:0006325 1.691165e-16 1 59
11744 GO:0044428 1.407598e-15 1 157
11740 GO:0044422 2.439226e-15 1 235
13920 GO:0051276 1.389881e-14 1 69
11225 GO:0043231 1.518125e-14 1 295
numInCat term ontology
11757 6649 intracellular organelle part CC
3148 723 chromatin organization BP
11744 3692 nuclear part CC
11740 6888 organelle part CC
13920 1058 chromosome organization BP
11225 9758 intracellular membrane-bounded organelle CC
category over_represented_pvalue under_represented_pvalue numDEInCat
3148 GO:0006325 1.691165e-16 1 59
13920 GO:0051276 1.389881e-14 1 69
4827 GO:0010467 2.738277e-14 1 184
5745 GO:0016070 3.046657e-14 1 164
17528 GO:0090304 4.206196e-14 1 177
5987 GO:0016569 9.534743e-14 1 48
numInCat term ontology
3148 723 chromatin organization BP
13920 1058 chromosome organization BP
4827 4871 gene expression BP
5745 4006 RNA metabolic process BP
17528 4471 nucleic acid metabolic process BP
5987 520 covalent chromatin modification BP
[1] 2
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
5178 GO:0012505 7.896233e-25 1 124
8223 GO:0031984 7.378768e-23 1 55
11755 GO:0044444 5.786768e-18 1 173
8221 GO:0031982 7.228745e-18 1 112
2833 GO:0005783 2.316476e-17 1 67
18199 GO:0098827 1.247675e-16 1 35
numInCat term ontology
5178 3583 endomembrane system CC
8223 802 organelle subcompartment CC
11755 7712 cytoplasmic part CC
8221 3918 vesicle CC
2833 1558 endoplasmic reticulum CC
18199 456 endoplasmic reticulum subcompartment CC
category over_represented_pvalue under_represented_pvalue numDEInCat
5349 GO:0015031 7.586032e-08 1.0000000 53
9629 GO:0034976 9.555774e-08 1.0000000 16
16645 GO:0071705 1.374311e-07 1.0000000 59
12003 GO:0045184 1.747714e-07 1.0000000 54
5634 GO:0015833 2.404955e-07 0.9999999 53
11032 GO:0042886 3.230345e-07 0.9999999 53
numInCat term ontology
5349 1761 protein transport BP
9629 217 response to endoplasmic reticulum stress BP
16645 2100 nitrogen compound transport BP
12003 1855 establishment of protein localization BP
5634 1807 peptide transport BP
11032 1823 amide transport BP
[1] 3
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
11766 GO:0044455 2.712250e-58 1 55
2801 GO:0005743 2.975123e-56 1 64
6727 GO:0019866 5.893037e-55 1 64
2798 GO:0005740 1.130974e-54 1 70
18184 GO:0098800 1.580494e-53 1 47
11225 GO:0043231 2.212897e-53 1 167
numInCat term ontology
11766 185 mitochondrial membrane part CC
2801 401 mitochondrial inner membrane CC
6727 442 organelle inner membrane CC
2798 606 mitochondrial envelope CC
18184 111 inner mitochondrial membrane protein complex CC
11225 9758 intracellular membrane-bounded organelle CC
category over_represented_pvalue under_represented_pvalue numDEInCat
8936 GO:0033108 4.372404e-27 1 25
12412 GO:0046034 5.049564e-26 1 30
4466 GO:0009167 3.405734e-25 1 30
4427 GO:0009126 4.304702e-25 1 30
4460 GO:0009161 5.329877e-25 1 30
9517 GO:0034622 6.795534e-25 1 47
numInCat term ontology
8936 71 mitochondrial respiratory chain complex assembly BP
12412 204 ATP metabolic process BP
4466 230 purine ribonucleoside monophosphate metabolic process BP
4427 231 purine nucleoside monophosphate metabolic process BP
4460 233 ribonucleoside monophosphate metabolic process BP
9517 902 cellular macromolecular complex assembly BP
[1] 4
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 5
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 6
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
11625 GO:0044238 2.036962e-06 0.9999994 62
11624 GO:0044237 2.393820e-06 0.9999992 62
16644 GO:0071704 4.209145e-06 0.9999986 63
3493 GO:0006807 6.113639e-06 0.9999979 59
18998 GO:1901564 6.803428e-06 0.9999976 45
numInCat term ontology
11625 9197 primary metabolic process BP
11624 9220 cellular metabolic process BP
16644 9689 organic substance metabolic process BP
3493 8654 nitrogen compound metabolic process BP
18998 5793 organonitrogen compound metabolic process BP
category over_represented_pvalue under_represented_pvalue numDEInCat
11625 GO:0044238 2.036962e-06 0.9999994 62
11624 GO:0044237 2.393820e-06 0.9999992 62
16644 GO:0071704 4.209145e-06 0.9999986 63
3493 GO:0006807 6.113639e-06 0.9999979 59
18998 GO:1901564 6.803428e-06 0.9999976 45
numInCat term ontology
11625 9197 primary metabolic process BP
11624 9220 cellular metabolic process BP
16644 9689 organic substance metabolic process BP
3493 8654 nitrogen compound metabolic process BP
18998 5793 organonitrogen compound metabolic process BP
[1] 7
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
995 GO:0002252 0 1 26
1075 GO:0002376 0 1 39
3585 GO:0006952 0 1 32
4698 GO:0009897 0 1 14
14118 GO:0051607 0 1 15
18072 GO:0098552 0 1 15
numInCat term ontology
995 651 immune effector process BP
1075 2168 immune system process BP
3585 1320 defense response BP
4698 309 external side of plasma membrane CC
14118 202 defense response to virus BP
18072 499 side of membrane CC
category over_represented_pvalue under_represented_pvalue numDEInCat
995 GO:0002252 0.000000e+00 1 26
1075 GO:0002376 0.000000e+00 1 39
3585 GO:0006952 0.000000e+00 1 32
14118 GO:0051607 0.000000e+00 1 15
11949 GO:0045087 5.199351e-20 1 23
14166 GO:0051707 8.569374e-20 1 25
numInCat term ontology
995 651 immune effector process BP
1075 2168 immune system process BP
3585 1320 defense response BP
14118 202 defense response to virus BP
11949 634 innate immune response BP
14166 832 response to other organism BP
[1] 8
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
15 GO:0000028 0 1 7
958 GO:0002181 0 1 13
1665 GO:0003676 0 1 41
1688 GO:0003723 0 1 41
1693 GO:0003729 0 1 12
1695 GO:0003735 0 1 38
numInCat term ontology
15 19 ribosomal small subunit assembly BP
958 58 cytoplasmic translation BP
1665 3418 nucleic acid binding MF
1688 1569 RNA binding MF
1693 213 mRNA binding MF
1695 147 structural constituent of ribosome MF
category over_represented_pvalue under_represented_pvalue numDEInCat
15 GO:0000028 0 1 7
958 GO:0002181 0 1 13
3204 GO:0006412 0 1 40
3279 GO:0006518 0 1 40
3493 GO:0006807 0 1 45
3999 GO:0008152 0 1 45
numInCat term ontology
15 19 ribosomal small subunit assembly BP
958 58 cytoplasmic translation BP
3204 604 translation BP
3279 753 peptide metabolic process BP
3493 8654 nitrogen compound metabolic process BP
3999 10180 metabolic process BP
[1] 9
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 10
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
11221 GO:0043227 2.855916e-07 1.0000000 43
11220 GO:0043226 8.367349e-07 0.9999999 44
11223 GO:0043229 1.105497e-06 0.9999998 42
11225 GO:0043231 1.123530e-06 0.9999998 39
8221 GO:0031982 4.139869e-06 0.9999990 23
numInCat term ontology
11221 11402 membrane-bounded organelle CC
11220 12318 organelle CC
11223 11275 intracellular organelle CC
11225 9758 intracellular membrane-bounded organelle CC
8221 3918 vesicle CC
[1] category over_represented_pvalue under_represented_pvalue
[4] numDEInCat numInCat term
[7] ontology
<0 rows> (or 0-length row.names)
[1] 11
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2874 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
11748 GO:0044432 7.285038e-09 1 11
2839 GO:0005789 1.460999e-08 1 10
18199 GO:0098827 1.939887e-08 1 10
10678 GO:0042175 2.188852e-08 1 10
2833 GO:0005783 2.721879e-08 1 16
8223 GO:0031984 4.433091e-08 1 12
numInCat term
11748 541 endoplasmic reticulum part
2839 443 endoplasmic reticulum membrane
18199 456 endoplasmic reticulum subcompartment
10678 462 nuclear outer membrane-endoplasmic reticulum membrane network
2833 1558 endoplasmic reticulum
8223 802 organelle subcompartment
ontology
11748 CC
2839 CC
18199 CC
10678 CC
2833 CC
8223 CC
category over_represented_pvalue under_represented_pvalue numDEInCat
9511 GO:0034613 2.136080e-06 0.9999997 14
16102 GO:0070727 2.316004e-06 0.9999996 14
14130 GO:0051641 2.628164e-06 0.9999995 17
3966 GO:0008104 1.348501e-05 0.9999973 16
13855 GO:0051179 3.543872e-05 0.9999909 24
numInCat term ontology
9511 1609 cellular protein localization BP
16102 1620 cellular macromolecule localization BP
14130 2452 cellular localization BP
3966 2461 protein localization BP
13855 5563 localization BP
